Contact

 pcherry [at] pm [dot] me |  upon request |  Senior Scientist | Oncology |  BillionToOne |  San Francisco, California |  pdcherry.github.io |  github.com/pdcherry |  linkedin.com/in/p-cherry |  United States Citizen |

Disclaimer

Last updated on 2024-12-10.

Data-driven CV made in R using pagedown.

Main

Patrick Cherry

PhD scientist and professional critical thinker, problem-solver, and science communicator. At the interface of data science, genomics, and statistics; skilled at data visualization, bioinformatics, next-generation sequencing (NGS), and tool-building. I’ve coded reproducible pipelines for high-throughput experimental designs and genomic analyses. I’ve launched best-in-class oncology reference standards and analyzed NGS data from Illumina, MGI, and Element. Originally trained in Molecular Biology, I am passionate about advancing data science and bioinformatics to improve human health and to understand biology.

Education

PhD

University of Colorado School of Medicine

Aurora/Denver, Colorado

May 2019 - Aug 2013

  • Ph.D. in Molecular Biology. Advisor: Jay Hesselberth, PhD
  • Thesis: RNA terminus chemistry impact decay events that target HAC1 mRNA during the Unfolded Protein Response

BA

Hendrix College

Conway, Arkansas

May 2013 - Aug 2009

  • Biochemistry and Molecular Biology, with Distinction. Advisor: Andres Caro, PhD
  • Senior Capstone Project showing key stress response gene expression changes to oxidative stress in liver cells
  • Minor in Mathematics; PI: Lars Seme; Project: Newton’s method as a fractal chaotic dynamical system

Industry Experience

I currently split my time between wet lab and computational activities. I have worked in a variety of roles ranging from HTP strain onboarding to genomics scientist. I like collaborative environments where I can learn from my peers and in turn teach others.

Senior Scientist, Oncology

BillionToOne

Menlo Park, CA

Current - Sep 2024

  • Generated 500+ automated ddPCR primer / probe designs with pipeline in snakemake using s3 database of variant data and primer3 primer selection
  • Informed key product decisions with historical analyses using PostgreSQL / ssh and s3 data sources and linear mixed-effects modeling

Senior Scientist, Genomics

Twist Bioscience

South San Francisco, California

Apr 2024 - Jan 2021

  • Invented and introduced multiple new products to market, yielding $1M+ in new revenue as Tech Lead, including: Pan-cancer cfDNA (v1 & v2), CNV Controls, RNA Fusion Controls, Fragmentome Controls, RNA-seq, and primer / adapter removal methods for highly-multiplexed dsDNA pools
  • Answered biological and business questions with DoE and data analysis using R and the libraries: dplyr, dbplyr, DBI, purrr, ggplot2, Bioconductor, DEseq2, seurat, tidymodels, glm, nls, lme4, AlgDesign, and more
  • Edited and maintained production QC pipelines with automated reporting using Python and the libraries: NumPy, pandas, polars, seaborn, statsmodels, biopython, pybedtools, pysam, vcfpy, scanpy, Jinja2 (with CSS), WeasyPrint,and others
  • Maintained production code (git version control with code review) with CD (github actions); operated in high-performance compute environment aws s3 and Databricks using Unix shell / bash tools, like ssh, STAR-fusion, GATK, BaseSpace CLI, bwa, bedtools, samtools, vcftools, UMI-tools/fgbio; Confluence documentation
  • Authored internal R package “twistcolorpal” on Github with help files to help scientists style plots to Twist branding
  • Answered production and business questions with original SQL queries for Snowflake-based database

Scientist I, NGS Core & Strain-Build Process Development

Zymergen, Inc.

Emeryville, California

Jan 2021 - Apr 2019

  • Boosted NGS Core genotyping success by 45% using DoE experimentation, data-driven decision-making, and teaching; Guided demanding and diverse internal customers on complex NGS experiments
  • Built and disseminated Rmarkdown and JMP statistical templates for autonomous NGS data exploration
  • Coded plasmid and strain build and QC experiments using Zymergen’s alembic Python API to LIMS database
  • Rendered strain build and plasmid build reports from LIMS SQL database in MySQL Workbench

Research Experience

I worked on a few projects during my PhD, and the RNA repair project led me to custom 5′-OH RNA-seq libraries, which inspired my fascination with transcriptomics and bioinformatics.

Doctoral Research

University of Colorado School of Medicine

Aurora/Denver, Colorado

May 2019 - May 2014

  • Wrote, revised, & published two academic papers on RNA repair & yeast genetics
  • Engineered and characterized genetic bypass of essential genes in budding yeast; on-boarded CRISPR/Cas9 for efficient and precise gene knock-in and scarless knock-out
  • Performed RNA-seq analysis with bowtie2 on departmental cluster using bjobs and visualization in R-Studio server
  • Optimized custom RNA-seq library protocol; independently planned, executed, troubleshooted RNA modification detection
  • Routinely conducted northern blotting, targeted depletion, primer extension, splinted ligation, and other esoteric DNA and RNA experiments

Undergraduate Research Assistant

Lab of Dr. Andres Caro, Hendrix College

Conway, Arkansas

Jan 2013 - Jan 2012

Summer Undergraduate Research Fellowship

Lab of Dr. Michael Shiloh, UT Southwestern Medical Center

Dallas, Texas

Jan 2012 - Jan 2012

Research Assistant

Lab of Dr. Joy Sturtevant, Louisiana Health Sciences Center

New Orleans, Louisiana

Jan 2011 - Jan 2010

Intellectual Property

Working at Twist and Zymergen on new product research requires confidentiality, but public evidence of accomplishments often comes in patent applications. The Legal teams know me well for being a helpful expert in the process.

Methylation-mediated adapter removal on nucleic acid sequences

Twist Bioscience

South San Francisco, California

Mar 2023

  • US 63-317,466

Expansion of cfDNA for Libraries

Twist Bioscience

South San Francisco, California

Nov 2021

  • US Prov. Pat. Ref No 823.102

Libraries for mutational analysis

Twist Bioscience

South San Francisco, California

Apr 2021

  • US Prov. Pat. Ref No 823.101
  • Configuration and fabrication of synthetic DNA & RNA reference standards and synthetic variant sequences

Method for counterselection in microorganisms

Zymergen, Inc.

Emeryville, California

Mar 2021

  • US 2021_0087586 A1
  • Demonstration of novel counterselection mechanism in non-model Bacillus microbe for genetic modification

Selected Publications

I communicate my results clearly, both in writing and in live presentations. I enjoy writing research papers, but my career has required more tech notes and app notes recently.

Twist cfDNA Pan-Cancer Reference Standard v2 Technical Guidance

Twist Bioscience Product Sheet & FAQ

South San Francisco, California

Jan 2024

  • Patrick Cherry, Lydia Bonar, & Mike Bocek

Characteristics and specificity of the wild-type / 0% VAF reference material

Twist Bioscience

South San Francisco, California

Apr 2022

  • Patrick Cherry & Mike Bocek

Twist Pan-cancer synthetic reference materials technical guide (deprecated)

Twist Bioscience

South San Francisco, California

Dec 2021

  • Patrick Cherry & Mike Bocek

Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response

eLife

Aurora/Denver, Colorado

Mar 2019

  • Cherry, P., Peach, S., & Hesselberth, J.

Genetic bypass of essential RNA repair enzymes in budding yeast

RNA

Aurora/Denver, Colorado

Dec 2017

  • Cherry, P., White, L., York, K., & Hesselberth, J.

Selected Presentations & Talks

I give audience-centered presentations by adapting on the fly and over time to the venue and occasion. I like to transfer knowledge by giving methods/best practices talks whose slides can also serve as documentation.

Twist pan-cancer reference standard V2: Enhanced precision and reduced errors in ctDNA analysis

Advances in Genome Biology and Technology, Twist Bioscience

Orlando, Florida

Feb 2024

  • Lydia Bonar, Patrick Cherry, Michael Bocek, Shawn Gorda, Derek Murphy, and Esteban Toro

High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring

International Society of Liquid Biopsy Annual Congress, Twist Bioscience

Madrid, Spain

Nov 2023

  • Tina Han, Tong Liu, Michael Bocek, Patrick Cherry, Shawn Gorda, Nairi Pezeshkian, Dan Nasko, Po-Yuan Tung, Derek Murphy, and Esteban Toro

High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring

American Association for Cancer Researchers, Twist Bioscience

Orlando, Florida

Apr 2023

  • Tong Liu, Michael Bocek, Patrick Cherry, Shawn Gorda, Jean Challacombe, Derek Murphy and Esteban Toro

An end-to-end workflow for accurate methylation detection

American Association for Cancer Researchers, Twist Bioscience

Orlando, Florida

Apr 2023

  • Lydia Bonar, Kristin Butcher, Michael Bocek, Holly Corbitt, Bryan Hoglund, Cibelle Nassif, Patrick Cherry, Derek Murphy, Jean Challacombe, Esteban Toro

Twist pan-cancer synthetic RNA fusion control for assay development

American Association for Cancer Researchers, Twist Bioscience

Orlando, Florida

Apr 2023

  • Patrick Cherry, Jason Corwin, Yu Cai, Kit Fuhrman, Jean Challacombe, Derek Murphy, Esteban Toro

Colorado RNA Club Industry Session

Colorado RNA Club

Boulder, Colorado

Apr 2023

Use of synthetic CNV fragments to mimic copy number alterations for ctDNA reference standards

Advances in Genome Biology and Technology, Twist Bioscience

Hollywood, Florida

Feb 2023

  • Jason Corwin, Patrick Cherry, Shawn Gorda, Michael Bocek, Jean Challacombe, Derek Murphy, Esteban Toro

Methylation Controls to detect for methylation level quantification in the Twist Targeted Methylation Sequencing workflow

Advances in Genome Biology and Technology

Hollywood, Florida

Feb 2023

  • Kristin Butcher, Michael Bocek, Patrick Cherry, Jean Challacombe, Esteban Toro

Efficient, high sensitivity detection of oncogenic variants with UMIs and target enrichment

European Human Genetics Conference

Vienna, Austria

May 2022

  • Michael Bocek, Lydia Bonar, Jean Challacombe, Richard Gantt, Patrick Cherry, Rebecca Liao, Derek Murphy and Esteban Toro

Twist pan-cancer synthetic reference materials for cell-free DNA (cfDNA) assay development

American Association for Cancer Researchers, Twist Bioscience

New Orleans, Louisiana

Apr 2022

Pan-cancer Reference Standard: Methods in Automation & Future Needs

Twist Automation Group Meeting

South San Francisco, CA

Apr 2022

Twist reference material products: current methods and future applications

Twist R&D Symposium

South San Francisco, CA

Mar 2022

Pan-cancer Reference Standard: Methods & Lessons from NPI & QC

Twist R&D Meeting

South San Francisco, CA

Feb 2022

Molecular Methods Meet the Standards: Or how I learned to stop worrying and love UV-quantification

Twist R&D Meeting

South San Francisco, CA

Jul 2021

Colorado RNA Club Industry Session

Colorado RNA Club

Boulder, Colorado

Apr 2021

R use at Zymergen

Z-Tech Talk

Emeryville, CA

Jun 2020

Data-driven troubleshooting of NGS experiments

Data Science Talk

Emeryville, CA

Apr 2020

NGS Sample Preparation Deep-Dive

NGS Technical Talk Series

Emeryville, CA

Mar 2020

RNA terminus chemistry potentiates decay events that target HAC1 mRNA during the unfolded protein response

Thesis Defense Seminar

Aurora, Colorado

Jan 2019

RNA modification and decay regulates the unfolded protein response

Rocky Mountain Yeast Meeting Poster

Fort Collins, Colorado

Jan 2019

What the unfolded protein response teaches us about RNA decay

Bolie Scholar Talk, Molecular Biology Program Retreat

Winter Park, CO

Oct 2018

Genetic bypass of essential yeast RNA repair enzymes

Rocky Mountain Yeast Meeting Poster

Golden, Colorado

Jan 2018

Genetic bypass of essential yeast RNA repair enzymes

Molecular Biology Program Update Talk

Aurora, Colorado

Oct 2017

RNA processing regulates the unfolded protein response

CSHL: mRNA Processing Meeting Talk

Cold Spring Harbor, New York

Aug 2017

Genetic bypass of essential yeast RNA repair enzymes

Rocky Mountain Yeast Meeting Poster

Boulder, Colorado

Jan 2017

RNA processing regulates the unfolded protein response

RNA Club Talk

Boulder, Colorado

Dec 2016

RNA Healing and Destruction

Molecular Biology Program Update Talk

Aurora, Colorado

Oct 2016

RNA processing regulates the unfolded protein response

Rocky Mountain Yeast Meeting Poster

Fort Collins, Colorado

Jan 2016

Turnover of endonucleolytic products of No-Go mRNA decay

RNA Stability Meeting

Estes Park, Colorado

Jun 2015

RNA 5′-kinase-mediated co-translational mRNA decay

Molecular Biology Program Update Talk

Aurora, Colorado

Feb 2015

RNA 5′-kinase-mediated co-translational mRNA decay

Rocky Mountain Yeast Meeting Poster

Aurora, Colorado

Jan 2015

RNA 5′-kinase-mediated co-translational mRNA decay

Rocky Mountain Yeast Meeting Poster

Boulder, Colorado

Jan 2014

Coordinated upregulation of antioxidant protection and mitochondrial DNA biosynthesis in liver cells by oxidative stress

Senior Undergraduate Capstone Research Talk

Conway, Arkansas

Jan 2013

Trainees & Direct Reports

While I’ve not held a role with “manager” in the title, all Scientist positions I’ve accepted have involved formal report management responsibility. I take managing and mentoring seriously; I emphasize trust, learning, and growth with my reports.

Derek Cai, BS, University of California San Diego, Research Associate I

Twist Bioscience

South San Francisco, California

Jan 2024 - Jan 2022

Lydia Bonar, MS, Johns Hopkins University, Scientist

Twist Bioscience

South San Francisco, California

Jan 2024 - Jan 2021

Alonzo Lee, BS, University of California Santa Cruz, Scientist

Twist Bioscience

South San Francisco, California

Jan 2022 - Jan 2021

Kaisle Hill, BA, University of California Berkeley, Senior Research Associate

Zymergen, Inc.

Emeryville, California

Jan 2021 - Jan 2020

Rachel A Jones, MS, University of Arizona, Postdoctoral Fellow

University of Colorado School of Medicine

Aurora/Denver, Colorado

Jan 2017

Laura K White, MS, Biotechnology, Johns Hopkins University, Postdoctoral Fellow

University of Colorado School of Medicine

Aurora/Denver, Colorado

Jan 2016

Haven Himmighoefer, Undergraduate, University of Colorado Denver

University of Colorado School of Medicine

Aurora/Denver, Colorado

Jan 2016 - Jan 2014

Leslie Aranda, Undergraduate, University of California Riverside

University of Colorado School of Medicine

Aurora/Denver, Colorado

Jan 2015